For example, the HSA worksheet lists 1000 from the employer in one box and the remaining contribution by myself (to get to the max for the year - $3450). After clicking Done on the worksheet, the deduction ONLY lists my contribution (it doesn't include what my employer contributed). This seems wrong as the individual max is 3450 which is exactly what was contributed.
The employer's contribution has already been deducted from the taxable income. Whenever you see a code W in Box 12 of Form W-2, they refer to pre-tax contributions to the HSA (whether your employer made the contribution or it was your election to have some of your pay be contributed to the HSA, it is the same treatment: a pre-tax contribution). Without that contribution, your box 1 amount would have been $1000 higher. (If the contribution came from your employer, it would not have affected your income but you still could not claim a deduction because you personally did not make the contribution).
But, since the $2450 was your out-of-pocket (and therefore after-tax) contribution, you do receive a deduction for this amount.
The employer's contribution has already been deducted from the taxable income. Whenever you see a code W in Box 12 of Form W-2, they refer to pre-tax contributions to the HSA (whether your employer made the contribution or it was your election to have some of your pay be contributed to the HSA, it is the same treatment: a pre-tax contribution). Without that contribution, your box 1 amount would have been $1000 higher. (If the contribution came from your employer, it would not have affected your income but you still could not claim a deduction because you personally did not make the contribution).
But, since the $2450 was your out-of-pocket (and therefore after-tax) contribution, you do receive a deduction for this amount.